Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1563
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63362
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:568 original size:3 final size:3
Alignment explanation
Indices: 560--589 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
550 GGTCCAAGGC
560 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
590 GGCCATCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1504 original size:17 final size:17
Alignment explanation
Indices: 1466--1504 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1456 TAAAATTAAT
*
1466 AAATATATTAATATATA
1 AAATTTATTAATATATA
1483 AAATTTATTCAATAT-TA
1 AAATTTATT-AATATATA
1500 AAATT
1 AAATT
1505 AGATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATTAATATATA
Found at i:10115 original size:39 final size:39
Alignment explanation
Indices: 10069--10150 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
10059 CTATAAGTTT
*
10069 TTCTCCTATTTTATTTGGAAACTAACGAAAACATACTAA
1 TTCTCCTATTTTATTTGGAAACAAACGAAAACATACTAA
10108 TTCTCCTATTTTATTTGGAAACAAACGAAAACATACTAA
1 TTCTCCTATTTTATTTGGAAACAAACGAAAACATACTAA
10147 TTCT
1 TTCT
10151 TTTTGTTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (39 bp):
TTCTCCTATTTTATTTGGAAACAAACGAAAACATACTAA
Found at i:10594 original size:16 final size:15
Alignment explanation
Indices: 10573--10616 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
10563 ATTTTTTCGG
*
10573 TTAATTATAATAAATA
1 TTAATTATAA-AAAAA
10589 TTAATTATAAAAAAA
1 TTAATTATAAAAAAA
*
10604 TTAA-AATAAAAAA
1 TTAATTATAAAAAA
10617 TAGATGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 8 0.31
15 8 0.31
16 10 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATTATAAAAAAA
Found at i:11047 original size:15 final size:15
Alignment explanation
Indices: 11027--11055 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11017 ATTGTGGATA
11027 TAATGAATATTATTG
1 TAATGAATATTATTG
11042 TAATGAATATTATT
1 TAATGAATATTATT
11056 CGTACATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TAATGAATATTATTG
Found at i:11924 original size:21 final size:21
Alignment explanation
Indices: 11890--11940 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
11880 TTTACATATC
*
11890 AAAT-AATTTATATTATAAAA
1 AAATAAATATATATTATAAAA
* *
11910 AAATAAATATATATTATTATA
1 AAATAAATATATATTATAAAA
*
11931 ATATAAATAT
1 AAATAAATAT
11941 TAAAACTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATAAATATATATTATAAAA
Found at i:12224 original size:44 final size:44
Alignment explanation
Indices: 12161--12250 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
12151 AATATTATAT
12161 TTAAGTTTAATTCAAATTCGATCGAGCTTTGTACACCAATGACA
1 TTAAGTTTAATTCAAATTCGATCGAGCTTTGTACACCAATGACA
12205 TTAAGTTTAATTCAAATTCGATCGAGCTTTGTACACCAATGACA
1 TTAAGTTTAATTCAAATTCGATCGAGCTTTGTACACCAATGACA
12249 TT
1 TT
12251 GGGTAGGGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (44 bp):
TTAAGTTTAATTCAAATTCGATCGAGCTTTGTACACCAATGACA
Found at i:13804 original size:24 final size:24
Alignment explanation
Indices: 13777--13822 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
13767 TGGGTTTTAT
*
13777 AGAGATAAACTTGGAGAGAGAGTA
1 AGAGATAAACTTGGAGAAAGAGTA
* *
13801 AGAGATGAAGTTGGAGAAAGAG
1 AGAGATAAACTTGGAGAAAGAG
13823 AGTGAAGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.37, T:0.15
Consensus pattern (24 bp):
AGAGATAAACTTGGAGAAAGAGTA
Found at i:14126 original size:25 final size:25
Alignment explanation
Indices: 14034--14111 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
14024 AACATATTTA
* *
14034 TAAATATTATTTTGTAAATTATACTTT
1 TAAATATTATTTT-TAAA-TATAATTC
*
14061 TAAA-ATTATTATTTCTAATATAATTC
1 TAAATATTATT-TTT-AAATATAATTC
14087 TAAATATTATTTTTAAATATAATTC
1 TAAATATTATTTTTAAATATAATTC
14112 ATTAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 10 0.23
26 20 0.45
27 14 0.32
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAATATTATTTTTAAATATAATTC
Found at i:14131 original size:25 final size:25
Alignment explanation
Indices: 14034--14131 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 25
14024 AACATATTTA
* *
14034 TAAATATTATTTTGTAAATTATACTT-T
1 TAAA-ATTATTTT-TATA-TATAATTCT
*
14061 TAAAATTATTATTTCTAATATAATTC-
1 TAAAATTATT-TTTAT-ATATAATTCT
*
14087 TAAATATTATTTTTAAATATAATTCAT
1 TAAA-ATTATTTTTATATATAATTC-T
14114 TAAAA-TATTTTTATATAT
1 TAAAATTATTTTTATATAT
14132 TCATTTTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
25 21 0.36
26 21 0.36
27 17 0.29
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAAATTATTTTTATATATAATTCT
Found at i:16325 original size:26 final size:26
Alignment explanation
Indices: 16278--16366 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
16268 TAATTAGAAT
16278 ACAATTATA-ATACATACACTAACAA
1 ACAATTATATATACATACACTAACAA
* * * *
16303 GCAATTATATGTACGTACACTAATAA
1 ACAATTATATATACATACACTAACAA
* *
16329 ACAATTATATATAGGCATGCACTAATAA
1 ACAATTATATATA--CATACACTAACAA
16357 ACAATTATAT
1 ACAATTATAT
16367 TAATTAATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
25 8 0.15
26 24 0.45
28 21 0.40
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (26 bp):
ACAATTATATATACATACACTAACAA
Found at i:18092 original size:19 final size:20
Alignment explanation
Indices: 18068--18127 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
18058 TTTGAATTTC
18068 AACAAT-TTGTATCGATACA
1 AACAATATTGTATCGATACA
*
18087 AACAATAACTGTATCGATACA
1 AACAAT-ATTGTATCGATACA
* * *
18108 TA-AGTGTTGTATCGATACA
1 AACAATATTGTATCGATACA
18127 A
1 A
18128 TGTATTGCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (20 bp):
AACAATATTGTATCGATACA
Found at i:18182 original size:20 final size:20
Alignment explanation
Indices: 18157--18209 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
18147 TGCCAAGGAA
18157 ATGTATCGATACATT-ACTCG
1 ATGTATCGATACATTGA-TCG
*
18177 ATGTATCGATACATTGATCT
1 ATGTATCGATACATTGATCG
*
18197 TTGTATCGATACA
1 ATGTATCGATACA
18210 ATCTGGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGATCG
Found at i:32149 original size:4 final size:4
Alignment explanation
Indices: 32142--32206 Score: 57
Period size: 4 Copynumber: 16.5 Consensus size: 4
32132 AAAAAAAGAG
*
32142 AACA AACA AACA AA-A AAAA TAACA AA-A AA-A AA-A AACAA AACA AACA
1 AACA AACA AACA AACA AACA -AACA AACA AACA AACA AAC-A AACA AACA
*
32188 AAGTA AACA AACA AACA AA
1 AA-CA AACA AACA AACA AA
32207 AAAAAGGGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
3 12 0.23
4 31 0.58
5 10 0.19
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.03
Consensus pattern (4 bp):
AACA
Found at i:32171 original size:13 final size:13
Alignment explanation
Indices: 32130--32211 Score: 58
Period size: 13 Copynumber: 6.4 Consensus size: 13
32120 TATCCTCCGC
* *
32130 AAAAAAAAAGAGA
1 AAAAAAAAACAAA
* *
32143 ACAAACAAAC-AA
1 AAAAAAAAACAAA
*
32155 AAAAAATAACAAA
1 AAAAAAAAACAAA
32168 AAAAAAAAACAAA
1 AAAAAAAAACAAA
* * **
32181 ACAAACAAAGTAA
1 AAAAAAAAACAAA
* *
32194 ACAAACAAACAAA
1 AAAAAAAAACAAA
32207 AAAAA
1 AAAAA
32212 GGGTCCGGAT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
12 8 0.15
13 45 0.85
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:32181 original size:9 final size:9
Alignment explanation
Indices: 32149--32211 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 9
32139 GAGAACAAAC
32149 AAACAAAAA
1 AAACAAAAA
* *
32158 AAA-TAACA
1 AAACAAAAA
32166 AAA-AAAAA
1 AAACAAAAA
*
32174 AAACAAAAC
1 AAACAAAAA
**
32183 AAACAAAGT
1 AAACAAAAA
*
32192 AAAC-AAAC
1 AAACAAAAA
32200 AAACAAAAA
1 AAACAAAAA
32209 AAA
1 AAA
32212 GGGTCCGGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 18 0.43
9 24 0.57
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.03
Consensus pattern (9 bp):
AAACAAAAA
Found at i:32184 original size:38 final size:39
Alignment explanation
Indices: 32130--32211 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 39
32120 TATCCTCCGC
* *
32130 AAAAAAAAAGAGAACAAACAAA-CAAA-AAAAATAACAAA
1 AAAAAAAAACAAAACAAACAAAGCAAACAAAAA-AACAAA
* *
32168 AAAAAAAAACAAAACAAACAAAGTAAACAAACAAACAAA
1 AAAAAAAAACAAAACAAACAAAGCAAACAAAAAAACAAA
32207 AAAAA
1 AAAAA
32212 GGGTCCGGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 20 0.53
39 14 0.37
40 4 0.11
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (39 bp):
AAAAAAAAACAAAACAAACAAAGCAAACAAAAAAACAAA
Found at i:33722 original size:28 final size:28
Alignment explanation
Indices: 33644--33755 Score: 143
Period size: 28 Copynumber: 4.0 Consensus size: 28
33634 CATTCCTCAT
* *
33644 CCTTCAAAAGCCCACAAGTTAGTGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * * *
33672 CTTTTCCAAAGTCCATAAGTCAGTGGCAA
1 C-CTTCAAAAGCCCACAAGTCAGTGGCAA
*
33701 CCTTCAAAAACCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
33729 CCTTCAAAAGCCCACAAGTCTGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
33756 TCTTTTTCCT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
28 48 0.69
29 22 0.31
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:33823 original size:34 final size:33
Alignment explanation
Indices: 33736--33927 Score: 190
Period size: 34 Copynumber: 5.8 Consensus size: 33
33726 CAACCTTCAA
* * *
33736 AAGCCCACAAGTCTGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
33769 AAGTCCACAACTCCGAGGCACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
33802 AAAGCCCACAACTTCGTGGCACC-TTTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * ** *
33835 AAGTCCACGACTTTGTAGCACCCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTTCCTTTT
* *
33869 AAGCCCACACCTCCGTGGCATCCCTTTTTCC-TAT
1 AAGCCCACAACTCCGTGGCA--CCTTTTTCCTTTT
*
33903 AAGTCCACAACTCCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
33928 AAGCCCAATA
Statistics
Matches: 132, Mismatches: 23, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
32 21 0.16
33 39 0.30
34 62 0.47
35 10 0.08
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:33856 original size:66 final size:68
Alignment explanation
Indices: 33735--33924 Score: 203
Period size: 66 Copynumber: 2.8 Consensus size: 68
33725 GCAACCTTCA
* * *
33735 AAAGCCCACAA-GTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGAGGCA-CCTTTTTCT
1 AAAGCCCACAACTTC-GTGGCATCCTTTTCCTTTTAAGTCCACAACTCCGAGGCACCCTTTTTCC
33798 TTTT
65 TTTT
* * **
33802 AAAGCCCACAACTTCGTGGCA-CCTTTTCTTTTTAAGTCCACGACTTTGTA-GCACCCTTTTTCC
1 AAAGCCCACAACTTCGTGGCATCCTTTTCCTTTTAAGTCCACAACTCCG-AGGCACCCTTTTTCC
33865 TTTT
65 TTTT
* * * *
33869 -AAGCCCACACCTCCGTGGCATCCCTTTTTCC-TATAAGTCCACAACTCCGTGGCACC
1 AAAGCCCACAACTTCGTGGCAT-CC-TTTTCCTTTTAAGTCCACAACTCCGAGGCACC
33925 TTTAAGCCCA
Statistics
Matches: 101, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
66 43 0.43
67 30 0.30
68 23 0.23
69 5 0.05
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (68 bp):
AAAGCCCACAACTTCGTGGCATCCTTTTCCTTTTAAGTCCACAACTCCGAGGCACCCTTTTTCCT
TTT
Found at i:34032 original size:49 final size:49
Alignment explanation
Indices: 33924--34408 Score: 505
Period size: 49 Copynumber: 9.8 Consensus size: 49
33914 TCCGTGGCAC
* *
33924 CTTTAAGCCCAATATCGCTGGCCTTGTATCAGCACATTGGCA--TTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
33971 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGACACATTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
34020 CTTTAAGACCAATGTCG-TCGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCT-GGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
34069 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC--CTTCAT
* *
34121 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
34170 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT
* * *
34222 TTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
34271 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CAT
* * * * ** *
34323 -TTCTAAGCCCAATGTCGTTGGTCTTGTCTCAGCACATTGGCA--TTCTT
1 CTT-TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * *
34370 CTTCAAGTCTAATGTAGCTGGCCATGAATCAGCACATTG
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTG
34409 TCATTCTTCG
Statistics
Matches: 375, Mismatches: 48, Indels: 30
0.83 0.11 0.07
Matches are distributed among these distances:
47 66 0.18
48 3 0.01
49 174 0.46
50 5 0.01
51 3 0.01
52 124 0.33
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:34159 original size:101 final size:101
Alignment explanation
Indices: 33924--34408 Score: 592
Period size: 101 Copynumber: 4.9 Consensus size: 101
33914 TCCGTGGCAC
* * * * *
33924 CTTTAAGCCCAATATCGCTGGCCTTGTATCAGCACATTGGCA--TTCATCTTTAAGTCCAATATT
1 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
*
33987 GCTGGCCTTGAATCAGCATATTGACA-C--ATTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTATTCAT
*
34020 CTTTAAGACCAATGTCGTCGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* *
34085 GCTGGCCTTGAATCAGCATATTGGCGCCTTCTTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTATTCAT
* * *
34121 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTC
1 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* * **
34186 GTTGGCCTTGAATCAGCACATTGGCACCTTAACCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTATTCAT
* * *
34222 TTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATC
1 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
* * *
34287 GTTGGCCTTGAATCAGCATATTGGCATCTT-TAACAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTAT-TCAT
* * ** * * * *
34323 -TTCTAAGCCCAATGTCGTTGGTCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAATGT
1 CTT-TAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
* * *
34385 AGCTGGCCATGAATCAGCACATTG
65 CGCTGGCCTTGAATCAGCATATTG
34409 TCATTCTTCG
Statistics
Matches: 339, Mismatches: 43, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
96 37 0.11
98 44 0.13
99 36 0.11
100 2 0.01
101 220 0.65
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCATATTGGCACCTTATTCAT
Found at i:34193 original size:150 final size:148
Alignment explanation
Indices: 33924--34408 Score: 588
Period size: 150 Copynumber: 3.3 Consensus size: 148
33914 TCCGTGGCAC
* * *
33924 CTTTAAGCCCAATATCGCTGGCCTTGTATCAGCACATT-G-G-CATTCATCTTTAAGTCCAATAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCCTTTCATCTTTAAGTCCAATAT
* * * *
33986 TGCTGGCCTTGAATCAGCATATTGACACATTCATCTTTAAGACCAATGTCGTCGGCCTTGAATCA
66 CGTTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCA
34051 GCACATTGGCACCTTCAT
131 GCACATTGGCACCTTCAT
* *
34069 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCTTCATCTTTAAGACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCC-T-TTCATCTTTAAGTCCAAT
* * * *
34134 GTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGAAT
64 ATCGTTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGTTGGCCTTGAAT
34199 CAGCACATTGGCACCTTAACCAT
129 CAGCACATTGGCACCTT---CAT
* * * *
34222 TTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT-ATCTTTAAGTCCAATAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCCTTTCATCTTTAAGTCCAATAT
* * * *
34286 CGTTGGCCTTGAATCAGCATATTGGCATCTTTAACAT-TTCTAAGCCCAATGTCGTTGGTCTTGT
66 CGTTGGCCTTGAATCAGCATATTGGCA-CATT--CATCTT-TAAGACCAATGTCGTTGGCCTTGA
* *
34350 CTCAGCACATTGGCA--TTCTT
127 ATCAGCACATTGGCACCTTCAT
* * * * *
34370 CTTCAAGTCTAATGTAGCTGGCCATGAATCAGCACATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG
34409 TCATTCTTCG
Statistics
Matches: 294, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
145 35 0.12
146 1 0.00
147 1 0.00
148 36 0.12
150 132 0.45
151 7 0.02
152 3 0.01
153 79 0.27
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (148 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCGCCTTTCATCTTTAAGTCCAATAT
CGTTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCA
GCACATTGGCACCTTCAT
Found at i:36964 original size:26 final size:26
Alignment explanation
Indices: 36921--37009 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
36911 TAATTAGAAT
36921 ACAATTATA-ATACGTACACTAACAA
1 ACAATTATATATACGTACACTAACAA
* * *
36946 GCAATTATATGTACGTACACTAATAA
1 ACAATTATATATACGTACACTAACAA
* * *
36972 ACAATTATATATAGGCATGCACTAATAA
1 ACAATTATATATA--CGTACACTAACAA
37000 ACAATTATAT
1 ACAATTATAT
37010 TAATTAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 8 0.15
26 25 0.46
28 21 0.39
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (26 bp):
ACAATTATATATACGTACACTAACAA
Found at i:46738 original size:2 final size:2
Alignment explanation
Indices: 46733--46763 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46723 TTTTTGTTTA
46733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46764 CTCAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52109 original size:6 final size:5
Alignment explanation
Indices: 52087--52145 Score: 59
Period size: 5 Copynumber: 11.6 Consensus size: 5
52077 TTTTTCTATT
* *
52087 AAAATG AAAAG AAAAG AATAAG AGAAG AAAAG AAAA- AAAAG GAAA- AAAAG
1 AAAA-G AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
52137 AAAAAG AAA
1 -AAAAG AAA
52146 GAGGGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
4 7 0.16
5 25 0.56
6 13 0.29
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:52131 original size:10 final size:9
Alignment explanation
Indices: 52093--52147 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
52083 TATTAAAATG
52093 AAAAGAAAA
1 AAAAGAAAA
*
52102 GAATAAGAGAAG
1 -AA-AAGA-AAA
52114 AAAAGAAAA
1 AAAAGAAAA
*
52123 AAAAGGAAA
1 AAAAGAAAA
52132 AAAAGAAAA
1 AAAAGAAAA
52141 AGAAAGA
1 A-AAAGA
52148 GGGAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 19 0.50
10 11 0.29
11 6 0.16
12 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:52156 original size:21 final size:19
Alignment explanation
Indices: 52093--52156 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
52083 TATTAAAATG
*
52093 AAAAGAAAAGAATAAGAGAA
1 AAAAGAAAAGAA-AAGGGAA
*
52113 GAAAAGAAAA-AAAAGGAAA
1 -AAAAGAAAAGAAAAGGGAA
52132 AAAAGAAAAAGAAAGAGGGAA
1 AAAAG-AAAAGAAA-AGGGAA
52153 AAAA
1 AAAA
52157 TTGAGTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 5 0.14
21 18 0.49
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAGAAAAGGGAA
Found at i:52706 original size:20 final size:20
Alignment explanation
Indices: 52653--52782 Score: 68
Period size: 20 Copynumber: 6.2 Consensus size: 20
52643 ATTCAACATC
*
52653 AATTTTAAATATTTTTTAGATAT
1 AATTTT-AA-ATTTTTTA-ATAA
52676 AATGTTT-AATTTTTTAATAA
1 AAT-TTTAAATTTTTTAATAA
**
52696 AATTTTAAATTTAAT-ATAA
1 AATTTTAAATTTTTTAATAA
* * * * * *
52715 TATATT-AATTATTCAACATC
1 AATTTTAAATTTTTTAATA-A
*
52735 AATTTTAAATATTTTTTGAATAT
1 AATTTT-AA-ATTTTTT-AATAA
*
52758 AATTTTTAATTTTTTAATAA
1 AATTTTAAATTTTTTAATAA
52778 AATTT
1 AATTT
52783 AAAGAATTAA
Statistics
Matches: 80, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
18 4 0.05
19 13 0.16
20 25 0.31
21 15 0.19
22 3 0.04
23 14 0.17
24 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTTTAAATTTTTTAATAA
Found at i:52729 original size:82 final size:83
Alignment explanation
Indices: 52617--52782 Score: 291
Period size: 82 Copynumber: 2.0 Consensus size: 83
52607 ATATCATTCA
52617 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTT-AGATATAATGT
1 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGA-ATATAATGT
52681 TTAATTTTTTAATAAAATT
65 TTAATTTTTTAATAAAATT
* *
52700 TTAAATTTAATATAAT-ATATTAATTATTCAACATCAATTTTAAATATTTTTTGAATATAATTTT
1 TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGAATATAATGTT
52764 TAATTTTTTAATAAAATT
66 TAATTTTTTAATAAAATT
52782 T
1 T
52783 AAAGAATTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
82 63 0.79
83 17 0.21
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (83 bp):
TTAAATTTAATATAATAATATTAATCATTCAACATCAATTTTAAATATTTTTTGAATATAATGTT
TAATTTTTTAATAAAATT
Found at i:52830 original size:29 final size:29
Alignment explanation
Indices: 52773--52830 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
52763 TTAATTTTTT
* *
52773 AATAAAATTTAAAGAATTAAATTATTTAA
1 AATAAAATTTAAAGAATTAAACTAATTAA
52802 AATAAAATATT-AA-AATTATAACTAATTAA
1 AATAAAAT-TTAAAGAATTA-AACTAATTAA
52831 TATTATCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.20
29 18 0.72
30 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
AATAAAATTTAAAGAATTAAACTAATTAA
Found at i:52991 original size:15 final size:15
Alignment explanation
Indices: 52971--53001 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52961 TAATTTTATA
52971 TAAATTATATTATCT
1 TAAATTATATTATCT
52986 TAAATTATATTATCT
1 TAAATTATATTATCT
53001 T
1 T
53002 TCATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTATATTATCT
Found at i:56485 original size:19 final size:19
Alignment explanation
Indices: 56461--56500 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
56451 TTGTTCTCTT
*
56461 ATCGCAAATCAGATCATTG
1 ATCGCAAATCAGATAATTG
56480 ATCGCAAATCAGATAATTG
1 ATCGCAAATCAGATAATTG
56499 AT
1 AT
56501 TTACTGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (19 bp):
ATCGCAAATCAGATAATTG
Found at i:58130 original size:21 final size:21
Alignment explanation
Indices: 58105--58158 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
58095 TTCAATAATT
*
58105 TGTATCGATACAAT-AGGGTAA
1 TGTATCGATACAATAAGTG-AA
58126 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
58146 TATATCGATACAA
1 TGTATCGATACAA
58159 GTCTGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:58293 original size:52 final size:52
Alignment explanation
Indices: 58214--58350 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
58204 TCTAGAATGA
** *
58214 AAATGTATTGATGCATTCTTCATTGTATCGATACATTCTAGGTTTTTGACCC
1 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
*
58266 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACTC
1 AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
* *
58318 AAATGTATAAATACATTCATCAATGTATCGATA
1 AAATGTATAAATGCATTCTTCAATGTATCGATA
58351 TATGCAAGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (52 bp):
AAATGTATAAATGCATTCTTCAATGTATCGATACATTCTAGGTTTTTGACCC
Done.